rs2965261

Positions:

• chr19-53272433-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.243 in 151,948 control chromosomes in the GnomAD database, including 4,722 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (4722 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53272433G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36935 AN: 151830 Hom.: 4721 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.243 AC: 36951 AN: 151948 Hom.: 4722 Cov.: 31 AF XY: 0.245 AC XY: 18180 AN XY: 74246

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.256

Alfa AF: 0.272 Hom.: 8015

Bravo AF: 0.240

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.64
DANN	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2965261; hg19: chr19-53775686;